Abstract 1025: OvaPrint - a novel cfDNA methylation liquid biopsy for cancer risk assessment in high grade serous ovarian carcinoma
Authors: David N. Buckley, Gerald Gooden, Lee Shulman, Monica Newman, Mona Guo, Ben Yi Tew, Lynda Roman, Juan Pablo Lewinger, Bodour Salhia
Journal: Cancer Research (2023)

Abstract Background: High grade serous ovarian carcinoma (HGSOC) is a highly lethal gynecologic malignancy with a typical 5-year survival rate of 40% or less when diagnosed with late-stage disease. There is currently no single effective screening tool for high risk or community-based risk assessment for HGSOC and multivariate tests for preselected patients are suboptimal. In women with a known pelvic mass, surgery followed pathological assessment is currently the only definitive way to diagnose HGSOC. About 15% of women with a suspicious mass will have HGSOC and less than 15% will present with stage 1 cancer. A liquid biopsy assay based on cell-free (cf)DNA enables non-invasive dynamic assessment of disease status in patients with cancer where cfDNA methylation is particularly promising for detection of early stage HGSOC. The goal of the current study is to develop a cfDNA methylation liquid biopsy that can be used for the screening and risk assessment for HGSOC. Methods: Tissue and plasma samples were acquired under informed consent from multiple commercial and academic sources. Reduced representation bisulfite sequencing (RRBS) was performed on 33 HGSOC tissues as well as 8 normal ovary and 13 normal fallopian tube controls. Differentially methylated regions (DMRs) were called between HGSOC and normal controls using metilene and DSS. DMR calls with p-values &amp;lt; 0.05 and |αβ| &amp;gt; 0.45 (n = 1677 DMRs) were used to generate a targeted tissue-based methylation assay using the myBaits® hybrid probe capture platform (Daicel Arbor Biosciences). Next, targeted enrichment was performed on bisulfite converted plasma cfDNA on an independent set of 84 HGSOC samples (27 stage 1, 20 stage 2, 37 stage 3) and 100 samples from patients with benign ovarian masses. Mean beta value across DMRs were used to train a novel cfDNA methylation classifier model called OvaPrintTM to discriminate HGSOC from benign masses using a repeated 3-fold cross validation approach to obtain an unbiased estimate of the performance of the classifier. The average cross validated score for each sample was used to generate a receiver operator characteristic (ROC) curve. Results. RRBS analysis on HGSOC tissue and normal tissue controls demonstrated excellent separation of HGSOC from normal tissue samples using the selected DMRs. OvaPrintTM testing in an independent cohort of 184 plasma samples discriminated HGSOC from benign tumors with a high sensitivity and specificity (area under curve (AUC) = 0.931) using cfDNA methylation. Conclusions: OvaPrintTM is a novel cfDNA methylation liquid biopsy that can be used for effective cancer risk assessment for HGSOC in women presenting with pelvic masses. Citation Format: David N. Buckley, Gerald Gooden, Lee Shulman, Monica Newman, Mona Guo, Ben Yi Tew, Lynda Roman, Juan Pablo Lewinger, Bodour Salhia. OvaPrint - a novel cfDNA methylation liquid biopsy for cancer risk assessment in high grade serous ovarian carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1025.